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Haghani NB, Lampe RH, Samuel BS, Chalasani SH, Matty MA. Identification and characterization of a skin microbiome on Caenorhabditis elegans suggests environmental microbes confer cuticle protection. Microbiol Spectr 2024:e0016924. [PMID: 38980017 DOI: 10.1128/spectrum.00169-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 06/10/2024] [Indexed: 07/10/2024] Open
Abstract
In the wild, C. elegans are emersed in environments teeming with a veritable menagerie of microorganisms. The C. elegans cuticular surface serves as a barrier and first point of contact with their microbial environments. In this study, we identify microbes from C. elegans natural habitats that associate with its cuticle, constituting a simple "skin microbiome." We rear our animals on a modified CeMbio, mCeMbio, a consortium of ecologically relevant microbes. We first combine standard microbiological methods with an adapted micro skin-swabbing tool to describe the skin-resident bacteria on the C. elegans surface. Furthermore, we conduct 16S rRNA gene sequencing studies to identify relative shifts in the proportion of mCeMbio bacteria upon surface-sterilization, implying distinct skin- and gut-microbiomes. We find that some strains of bacteria, including Enterobacter sp. JUb101, are primarily found on the nematode skin, while others like Stenotrophomonas indicatrix JUb19 and Ochrobactrum vermis MYb71 are predominantly found in the animal's gut. Finally, we show that this skin microbiome promotes host cuticle integrity in harsh environments. Together, we identify a skin microbiome for the well-studied nematode model and propose its value in conferring host fitness advantages in naturalized contexts. IMPORTANCE The genetic model organism C. elegans has recently emerged as a tool for understanding host-microbiome interactions. Nearly all of these studies either focus on pathogenic or gut-resident microbes. Little is known about the existence of native, nonpathogenic skin microbes or their function. We demonstrate that members of a modified C. elegans model microbiome, mCeMbio, can adhere to the animal's cuticle and confer protection from noxious environments. We combine a novel micro-swab tool, the first 16S microbial sequencing data from relatively unperturbed C. elegans, and physiological assays to demonstrate microbially mediated protection of the skin. This work serves as a foundation to explore wild C. elegans skin microbiomes and use C. elegans as a model for skin research.
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Affiliation(s)
- Nadia B Haghani
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
- University of California San Diego, La Jolla, California, USA
| | - Robert H Lampe
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California, USA
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
| | - Buck S Samuel
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Sreekanth H Chalasani
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
- University of California San Diego, La Jolla, California, USA
| | - Molly A Matty
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
- Biology, University of Portland, Portland, Oregon, USA
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2
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Haley JA, Chalasani SH. C. elegans foraging as a model for understanding the neuronal basis of decision-making. Cell Mol Life Sci 2024; 81:252. [PMID: 38849591 DOI: 10.1007/s00018-024-05223-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/27/2024] [Accepted: 03/30/2024] [Indexed: 06/09/2024]
Abstract
Animals have evolved to seek, select, and exploit food sources in their environment. Collectively termed foraging, these ubiquitous behaviors are necessary for animal survival. As a foundation for understanding foraging, behavioral ecologists established early theoretical and mathematical frameworks which have been subsequently refined and supported by field and laboratory studies of foraging animals. These simple models sought to explain how animals decide which strategies to employ when locating food, what food items to consume, and when to explore the environment for new food sources. These foraging decisions involve integration of prior experience with multimodal sensory information about the animal's current environment and internal state. We suggest that the nematode Caenorhabditis elegans is well-suited for a high-resolution analysis of complex goal-oriented behaviors such as foraging. We focus our discussion on behavioral studies highlighting C. elegans foraging on bacteria and summarize what is known about the underlying neuronal and molecular pathways. Broadly, we suggest that this simple model system can provide a mechanistic understanding of decision-making and present additional avenues for advancing our understanding of complex behavioral processes.
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Affiliation(s)
- Jessica A Haley
- Neurosciences Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Sreekanth H Chalasani
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
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3
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Alkan C, Brésard G, Frézal L, Richaud A, Ruaud A, Zhang G, Félix MA. Natural variation in infection specificity of Caenorhabditis briggsae isolates by two RNA viruses. PLoS Pathog 2024; 20:e1012259. [PMID: 38861582 PMCID: PMC11195985 DOI: 10.1371/journal.ppat.1012259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/24/2024] [Accepted: 05/14/2024] [Indexed: 06/13/2024] Open
Abstract
Antagonistic relationships such as host-virus interactions potentially lead to rapid evolution and specificity in interactions. The Orsay virus is so far the only horizontal virus naturally infecting the nematode C. elegans. In contrast, several related RNA viruses infect its congener C. briggsae, including Santeuil (SANTV) and Le Blanc (LEBV) viruses. Here we focus on the host's intraspecific variation in sensitivity to these two intestinal viruses. Many temperate-origin C. briggsae strains, including JU1264 and JU1498, are sensitive to both, while many tropical strains, such as AF16, are resistant to both. Interestingly, some C. briggsae strains exhibit a specific resistance, such as the HK104 strain, specifically resistant to LEBV. The viral sensitivity pattern matches the strains' geographic and genomic relationships. The heavily infected strains mount a seemingly normal small RNA response that is insufficient to suppress viral infection, while the resistant strains show no small RNA response, suggesting an early block in viral entry or replication. We use a genetic approach from the host side to map genomic regions participating in viral resistance polymorphisms. Using Advanced Intercrossed Recombinant Inbred Lines (RILs) between virus-resistant AF16 and SANTV-sensitive HK104, we detect Quantitative Trait Loci (QTLs) on chromosomes IV and III. Building RILs between virus-sensitive JU1498 and LEBV-resistant HK104 followed by bulk segregant analysis, we identify a chromosome II QTL. In both cases, further introgressions of the regions confirmed the QTLs. This diversity provides an avenue for studying virus entry, replication, and exit mechanisms, as well as host-virus specificity and the host response to a specific virus infection.
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Affiliation(s)
- Cigdem Alkan
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Gautier Brésard
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Lise Frézal
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques Paris, Paris, France
| | - Aurélien Richaud
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Albane Ruaud
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Gaotian Zhang
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Marie-Anne Félix
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
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Singh A, Luallen RJ. Understanding the factors regulating host-microbiome interactions using Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230059. [PMID: 38497260 PMCID: PMC10945399 DOI: 10.1098/rstb.2023.0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/01/2024] [Indexed: 03/19/2024] Open
Abstract
The Human Microbiome Project was a research programme that successfully identified associations between microbial species and healthy or diseased individuals. However, a major challenge identified was the absence of model systems for studying host-microbiome interactions, which would increase our capacity to uncover molecular interactions, understand organ-specificity and discover new microbiome-altering health interventions. Caenorhabditis elegans has been a pioneering model organism for over 70 years but was largely studied in the absence of a microbiome. Recently, ecological sampling of wild nematodes has uncovered a large amount of natural genetic diversity as well as a slew of associated microbiota. The field has now explored the interactions of C. elegans with its associated gut microbiome, a defined and non-random microbial community, highlighting its suitability for dissecting host-microbiome interactions. This core microbiome is being used to study the impact of host genetics, age and stressors on microbiome composition. Furthermore, single microbiome species are being used to dissect molecular interactions between microbes and the animal gut. Being amenable to health altering genetic and non-genetic interventions, C. elegans has emerged as a promising system to generate and test new hypotheses regarding host-microbiome interactions, with the potential to uncover novel paradigms relevant to other systems. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- Anupama Singh
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Robert J. Luallen
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
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5
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González R, Félix MA. Caenorhabditis elegans immune responses to microsporidia and viruses. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 154:105148. [PMID: 38325500 DOI: 10.1016/j.dci.2024.105148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 01/30/2024] [Accepted: 02/03/2024] [Indexed: 02/09/2024]
Abstract
The model organism Caenorhabditis elegans is susceptible to infection by obligate intracellular pathogens, specifically microsporidia and viruses. These intracellular pathogens infect intestinal cells, or, for some microsporidia, epidermal cells. Strikingly, intestinal cell infections by viruses or microsporidia trigger a common transcriptional response, activated in part by the ZIP-1 transcription factor. Among the strongest activated genes in this response are ubiquitin-pathway members and members of the pals family, an intriguing gene family with cross-regulations of different members of genomic clusters. Some of the induced genes participate in host defense against the pathogens, for example through ubiquitin-mediated inhibition. Other mechanisms defend the host specifically against viral infections, including antiviral RNA interference and uridylation. These various immune responses are altered by environmental factors and by intraspecific genetic variation of the host. These pathogens were first isolated 15 years ago and much remains to be discovered using C. elegans genetics; also, other intracellular pathogens of C. elegans may yet to be discovered.
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Affiliation(s)
- Rubén González
- Institut de Biologie de l'École Normale Supérieure, CNRS, INSERM, 75005, Paris, France.
| | - Marie-Anne Félix
- Institut de Biologie de l'École Normale Supérieure, CNRS, INSERM, 75005, Paris, France
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Pires da Silva A, Kelleher R, Reynoldson L. Decoding lifespan secrets: the role of the gonad in Caenorhabditis elegans aging. FRONTIERS IN AGING 2024; 5:1380016. [PMID: 38605866 PMCID: PMC11008531 DOI: 10.3389/fragi.2024.1380016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024]
Abstract
The gonad has become a central organ for understanding aging in C. elegans, as removing the proliferating stem cells in the germline results in significant lifespan extension. Similarly, when starvation in late larval stages leads to the quiescence of germline stem cells the adult nematode enters reproductive diapause, associated with an extended lifespan. This review summarizes recent advancements in identifying the mechanisms behind gonad-mediated lifespan extension, including comparisons with other nematodes and the role of lipid signaling and transcriptional changes. Given that the gonad also mediates lifespan regulation in other invertebrates and vertebrates, elucidating the underlying mechanisms may help to gain new insights into the mechanisms and evolution of aging.
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González R, Félix MA. Caenorhabditis elegans defective-pharynx and constipated mutants are resistant to Orsay virus infection. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001166. [PMID: 38590801 PMCID: PMC10999980 DOI: 10.17912/micropub.biology.001166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/12/2024] [Accepted: 03/21/2024] [Indexed: 04/10/2024]
Abstract
C. elegans animals with a compromised pharynx accumulate bacteria in their intestinal lumen and activate a transcriptional response that includes anti-bacterial response genes. In this study, we demonstrate that animals with defective pharynxes are resistant to Orsay virus (OrV) infection. This resistance is observed for animals grown on Escherichia coli OP50 and on Comamonas BIGb0172, a bacterium naturally associated with C. elegans . The viral resistance observed in defective-pharynx mutants does not seem to result from constitutive transcriptional immune responses against viruses. OrV resistance is also observed in mutants with defective defecation, which share with the pharynx-defective perturbations in the regulation of their intestinal contents and altered lipid metabolism. The underlying mechanisms of viral resistance in pharynx- and defecation-defective mutants remain elusive.
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Affiliation(s)
- Rubén González
- Institut de Biologie de l’École Normale Supérieure-CNRS-INSERM, 75005 Paris, France
| | - Marie-Anne Félix
- Institut de Biologie de l’École Normale Supérieure-CNRS-INSERM, 75005 Paris, France
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Sengupta T, St. Ange J, Kaletsky R, Moore RS, Seto RJ, Marogi J, Myhrvold C, Gitai Z, Murphy CT. A natural bacterial pathogen of C. elegans uses a small RNA to induce transgenerational inheritance of learned avoidance. PLoS Genet 2024; 20:e1011178. [PMID: 38547071 PMCID: PMC10977744 DOI: 10.1371/journal.pgen.1011178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/09/2024] [Indexed: 04/02/2024] Open
Abstract
C. elegans can learn to avoid pathogenic bacteria through several mechanisms, including bacterial small RNA-induced learned avoidance behavior, which can be inherited transgenerationally. Previously, we discovered that a small RNA from a clinical isolate of Pseudomonas aeruginosa, PA14, induces learned avoidance and transgenerational inheritance of that avoidance in C. elegans. Pseudomonas aeruginosa is an important human pathogen, and there are other Pseudomonads in C. elegans' natural habitat, but it is unclear whether C. elegans ever encounters PA14-like bacteria in the wild. Thus, it is not known if small RNAs from bacteria found in C. elegans' natural habitat can also regulate host behavior and produce heritable behavioral effects. Here we screened a set of wild habitat bacteria, and found that a pathogenic Pseudomonas vranovensis strain isolated from the C. elegans microbiota, GRb0427, regulates worm behavior: worms learn to avoid this pathogenic bacterium following exposure, and this learned avoidance is inherited for four generations. The learned response is entirely mediated by bacterially-produced small RNAs, which induce avoidance and transgenerational inheritance, providing further support that such mechanisms of learning and inheritance exist in the wild. We identified Pv1, a small RNA expressed in P. vranovensis, that has a 16-nucleotide match to an exon of the C. elegans gene maco-1. Pv1 is both necessary and sufficient to induce learned avoidance of Grb0427. However, Pv1 also results in avoidance of a beneficial microbiome strain, P. mendocina. Our findings suggest that bacterial small RNA-mediated regulation of host behavior and its transgenerational inheritance may be functional in C. elegans' natural environment, and that this potentially maladaptive response may favor reversal of the transgenerational memory after a few generations. Our data also suggest that different bacterial small RNA-mediated regulation systems evolved independently, but define shared molecular features of bacterial small RNAs that produce transgenerationally-inherited effects.
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Affiliation(s)
- Titas Sengupta
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Jonathan St. Ange
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Rachel Kaletsky
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Rebecca S. Moore
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Renee J. Seto
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Jacob Marogi
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Coleen T. Murphy
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
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Slowinski SP, Gresham JD, Cui ER, Haspel K, Lively CM, Morran LT. Outcrossing in Caenorhabditis elegans increases in response to food limitation. Ecol Evol 2024; 14:e11166. [PMID: 38516572 PMCID: PMC10954511 DOI: 10.1002/ece3.11166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 02/05/2024] [Accepted: 02/29/2024] [Indexed: 03/23/2024] Open
Abstract
Theory predicts that organisms should diversify their offspring when faced with a stressful environment. This prediction has received empirical support across diverse groups of organisms and stressors. For example, when encountered by Caenorhabditis elegans during early development, food limitation (a common environmental stressor) induces the nematodes to arrest in a developmental stage called dauer and to increase their propensity to outcross when they are subsequently provided with food and enabled to develop to maturity. Here we tested whether food limitation first encountered during late development/early adulthood can also induce increased outcrossing propensity in C. elegans. Previously well-fed C. elegans increased their propensity to outcross when challenged with food limitation during the final larval stage of development and into early adulthood, relative to continuously well-fed (control) nematodes. Our results thus support previous research demonstrating that the stress of food limitation can induce increased outcrossing propensity in C. elegans. Furthermore, our results expand on previous work by showing that food limitation can still increase outcrossing propensity even when it is not encountered until late development, and this can occur independently of the developmental and gene expression changes associated with dauer.
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Affiliation(s)
- Samuel P. Slowinski
- Department of BiologyIndiana UniversityBloomingtonIndianaUSA
- Department BiologyUniversity of MarylandCollege ParkMarylandUSA
| | | | - Eric R. Cui
- Department of BiologyIndiana UniversityBloomingtonIndianaUSA
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10
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Indong RA, Park JM, Hong JK, Lyou ES, Han T, Hong JK, Lee TK, Lee JI. A simple protocol for cultivating the bacterivorous soil nematode Caenorhabditis elegans in its natural ecology in the laboratory. Front Microbiol 2024; 15:1347797. [PMID: 38476935 PMCID: PMC10929012 DOI: 10.3389/fmicb.2024.1347797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/09/2024] [Indexed: 03/14/2024] Open
Abstract
The complex interplay between an animal and its surrounding environment requires constant attentive observation in natural settings. Moreover, how ecological interactions are affected by an animal's genes is difficult to ascertain outside the laboratory. Genetic studies with the bacterivorous nematode Caenorhabditis elegans have elucidated numerous relationships between genes and functions, such as physiology, behaviors, and lifespan. However, these studies use standard laboratory culture that does not reflect C. elegans true ecology. C. elegans is found growing in nature and reproduced in large numbers in soils enriched with rotting fruit or vegetation, a source of abundant and diverse microbes that nourish the thriving populations of nematodes. We developed a simple mesocosm we call soil-fruit-natural-habitat that simulates the natural ecology of C. elegans in the laboratory. Apples were placed on autoclaved potted soils, and after a soil microbial solution was added, the mesocosm was subjected to day-night, temperature, and humidity cycling inside a growth chamber. After a period of apple-rotting, C elegans were added, and the growing worm population was observed. We determined optimal conditions for the growth of C. elegans and then performed an ecological succession experiment observing worm populations every few days. Our data showed that the mesocosm allows abundant growth and reproduction of C. elegans that resembles populations of the nematode found in rotting fruit in nature. Overall, our study presents a simple protocol that allows the cultivation of C. elegans in a natural habitat in the laboratory for a broad group of scientists to study various aspects of animal and microbial ecology.
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Affiliation(s)
- Rocel Amor Indong
- Division of Biological Science and Technology, Yonsei University Mirae Campus, Wonju, Republic of Korea
| | - Jong Min Park
- Division of Biological Science and Technology, Yonsei University Mirae Campus, Wonju, Republic of Korea
| | - Jin-Kyung Hong
- Department of Environmental and Energy Engineering, Yonsei University Mirae Campus, Wonju, Republic of Korea
| | - Eun Sun Lyou
- Department of Environmental and Energy Engineering, Yonsei University Mirae Campus, Wonju, Republic of Korea
| | - Taeman Han
- Korea National Park Research Insitute, Korea National Park Service, Wonju, Republic of Korea
| | - Jong Kwang Hong
- Division of Biological Science and Technology, Yonsei University Mirae Campus, Wonju, Republic of Korea
| | - Tae Kwon Lee
- Department of Environmental and Energy Engineering, Yonsei University Mirae Campus, Wonju, Republic of Korea
| | - Jin I. Lee
- Division of Biological Science and Technology, Yonsei University Mirae Campus, Wonju, Republic of Korea
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11
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Ding SS, Fox JL, Gordus A, Joshi A, Liao JC, Scholz M. Fantastic beasts and how to study them: rethinking experimental animal behavior. J Exp Biol 2024; 227:jeb247003. [PMID: 38372042 PMCID: PMC10911175 DOI: 10.1242/jeb.247003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Humans have been trying to understand animal behavior at least since recorded history. Recent rapid development of new technologies has allowed us to make significant progress in understanding the physiological and molecular mechanisms underlying behavior, a key goal of neuroethology. However, there is a tradeoff when studying animal behavior and its underlying biological mechanisms: common behavior protocols in the laboratory are designed to be replicable and controlled, but they often fail to encompass the variability and breadth of natural behavior. This Commentary proposes a framework of 10 key questions that aim to guide researchers in incorporating a rich natural context into their experimental design or in choosing a new animal study system. The 10 questions cover overarching experimental considerations that can provide a template for interspecies comparisons, enable us to develop studies in new model organisms and unlock new experiments in our quest to understand behavior.
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Affiliation(s)
- Siyu Serena Ding
- Max Planck Institute of Animal Behavior, 78464 Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78464 Konstanz, Germany
| | - Jessica L. Fox
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Andrew Gordus
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Abhilasha Joshi
- Departments of Physiology and Psychiatry, University of California, San Francisco, CA 94158, USA
| | - James C. Liao
- Department of Biology, The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Monika Scholz
- Max Planck Research Group Neural Information Flow, Max Planck Institute for Neurobiology of Behavior – caesar, 53175 Bonn, Germany
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Meisel JD, Miranda M, Skinner OS, Wiesenthal PP, Wellner SM, Jourdain AA, Ruvkun G, Mootha VK. Hypoxia and intra-complex genetic suppressors rescue complex I mutants by a shared mechanism. Cell 2024; 187:659-675.e18. [PMID: 38215760 PMCID: PMC10919891 DOI: 10.1016/j.cell.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 09/09/2023] [Accepted: 12/05/2023] [Indexed: 01/14/2024]
Abstract
The electron transport chain (ETC) of mitochondria, bacteria, and archaea couples electron flow to proton pumping and is adapted to diverse oxygen environments. Remarkably, in mice, neurological disease due to ETC complex I dysfunction is rescued by hypoxia through unknown mechanisms. Here, we show that hypoxia rescue and hyperoxia sensitivity of complex I deficiency are evolutionarily conserved to C. elegans and are specific to mutants that compromise the electron-conducting matrix arm. We show that hypoxia rescue does not involve the hypoxia-inducible factor pathway or attenuation of reactive oxygen species. To discover the mechanism, we use C. elegans genetic screens to identify suppressor mutations in the complex I accessory subunit NDUFA6/nuo-3 that phenocopy hypoxia rescue. We show that NDUFA6/nuo-3(G60D) or hypoxia directly restores complex I forward activity, with downstream rescue of ETC flux and, in some cases, complex I levels. Additional screens identify residues within the ubiquinone binding pocket as being required for the rescue by NDUFA6/nuo-3(G60D) or hypoxia. This reveals oxygen-sensitive coupling between an accessory subunit and the quinone binding pocket of complex I that can restore forward activity in the same manner as hypoxia.
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Affiliation(s)
- Joshua D Meisel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Maria Miranda
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Owen S Skinner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Presli P Wiesenthal
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Sandra M Wellner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alexis A Jourdain
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA.
| | - Vamsi K Mootha
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA.
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13
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Crombie TA, McKeown R, Moya ND, Evans K, Widmayer S, LaGrassa V, Roman N, Tursunova O, Zhang G, Gibson S, Buchanan C, Roberto N, Vieira R, Tanny R, Andersen E. CaeNDR, the Caenorhabditis Natural Diversity Resource. Nucleic Acids Res 2024; 52:D850-D858. [PMID: 37855690 PMCID: PMC10767927 DOI: 10.1093/nar/gkad887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/30/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
Studies of model organisms have provided important insights into how natural genetic differences shape trait variation. These discoveries are driven by the growing availability of genomes and the expansive experimental toolkits afforded to researchers using these species. For example, Caenorhabditis elegans is increasingly being used to identify and measure the effects of natural genetic variants on traits using quantitative genetics. Since 2016, the C. elegans Natural Diversity Resource (CeNDR) has facilitated many of these studies by providing an archive of wild strains, genome-wide sequence and variant data for each strain, and a genome-wide association (GWA) mapping portal for the C. elegans community. Here, we present an updated platform, the Caenorhabditis Natural Diversity Resource (CaeNDR), that enables quantitative genetics and genomics studies across the three Caenorhabditis species: C. elegans, C. briggsae and C. tropicalis. The CaeNDR platform hosts several databases that are continually updated by the addition of new strains, whole-genome sequence data and annotated variants. Additionally, CaeNDR provides new interactive tools to explore natural variation and enable GWA mappings. All CaeNDR data and tools are accessible through a freely available web portal located at caendr.org.
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Affiliation(s)
- Timothy A Crombie
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Ryan McKeown
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Nicolas D Moya
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
- Cell, Molecular, Developmental biology, and Biophysics Graduate Program, ohns Hopkins University, Baltimore, MD, USA
| | - Kathryn S Evans
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Samuel J Widmayer
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Vincent LaGrassa
- Northwestern University Information Technology, Media and Technology Innovation, Northwestern University, Evanston, IL USA
| | - Natalie Roman
- Northwestern University Information Technology, Media and Technology Innovation, Northwestern University, Evanston, IL USA
| | - Orzu Tursunova
- Northwestern University Information Technology, Media and Technology Innovation, Northwestern University, Evanston, IL USA
| | - Gaotian Zhang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Sophia B Gibson
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Claire M Buchanan
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Nicole M Roberto
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Rodolfo Vieira
- Northwestern University Information Technology, Media and Technology Innovation, Northwestern University, Evanston, IL USA
| | - Robyn E Tanny
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Erik C Andersen
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
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14
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Kirchweger B, Zwirchmayr J, Grienke U, Rollinger JM. The role of Caenorhabditis elegans in the discovery of natural products for healthy aging. Nat Prod Rep 2023; 40:1849-1873. [PMID: 37585263 DOI: 10.1039/d3np00021d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Covering: 2012 to 2023The human population is aging. Thus, the greatest risk factor for numerous diseases, such as diabetes, cancer and neurodegenerative disorders, is increasing worldwide. Age-related diseases do not typically occur in isolation, but as a result of multi-factorial causes, which in turn require holistic approaches to identify and decipher the mode of action of potential remedies. With the advent of C. elegans as the primary model organism for aging, researchers now have a powerful in vivo tool for identifying and studying agents that effect lifespan and health span. Natural products have been focal research subjects in this respect. This review article covers key developments of the last decade (2012-2023) that have led to the discovery of natural products with healthy aging properties in C. elegans. We (i) discuss the state of knowledge on the effects of natural products on worm aging including methods, assays and involved pathways; (ii) analyze the literature on natural compounds in terms of their molecular properties and the translatability of effects on mammals; (iii) examine the literature on multi-component mixtures with special attention to the studied organisms, extraction methods and efforts regarding the characterization of their chemical composition and their bioactive components. (iv) We further propose to combine small in vivo model organisms such as C. elegans and sophisticated analytical approaches ("wormomics") to guide the way to dissect complex natural products with anti-aging properties.
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Affiliation(s)
- Benjamin Kirchweger
- Division of Pharmacognosy, Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria.
| | - Julia Zwirchmayr
- Division of Pharmacognosy, Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria.
| | - Ulrike Grienke
- Division of Pharmacognosy, Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria.
| | - Judith M Rollinger
- Division of Pharmacognosy, Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria.
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15
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Ivanova M, Moss EG. Orthologs of the Caenorhabditis elegans heterochronic genes have divergent functions in Caenorhabditis briggsae. Genetics 2023; 225:iyad177. [PMID: 37788363 PMCID: PMC10697817 DOI: 10.1093/genetics/iyad177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 05/22/2023] [Accepted: 09/14/2023] [Indexed: 10/05/2023] Open
Abstract
The heterochronic genes of Caenorhabditis elegans comprise the best-studied pathway controlling the timing of tissue and organ formation in an animal. To begin to understand the evolution of this pathway and the significance of the relationships among its components, we characterized 11 Caenorhabditis briggsae orthologs of C. elegans heterochronic genes. Using CRISPR/Cas9, we made a variety of alleles and found that several mutant phenotypes differ in significant ways from those of C. elegans. Although most mutant orthologs displayed defects in developmental timing, their phenotypes could differ in which stages were affected, the penetrance and expressivity of the phenotypes, or by having additional pleiotropies that were not obviously connected to developmental timing. However, when examining pairwise epistasis and synergistic relationships, we found those paralleled the known relationships between their C. elegans orthologs, suggesting that the arrangements of these genes in functional modules are conserved, but the modules' relationships to each other and/or to their targets has drifted since the time of the species' last common ancestor. Furthermore, our investigation has revealed a relationship between this pathway to other aspects of the animal's growth and development, including gonad development, which is relevant to both species.
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Affiliation(s)
- Maria Ivanova
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering and Sciences, Rowan University, Stratford, NJ 08084, USA
| | - Eric G Moss
- Department of Molecular Biology, Rowan University, Stratford, NJ 08084, USA
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16
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Frézal L, Saglio M, Zhang G, Noble L, Richaud A, Félix MA. Genome-wide association and environmental suppression of the mortal germline phenotype of wild C. elegans. EMBO Rep 2023; 24:e58116. [PMID: 37983674 DOI: 10.15252/embr.202358116] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/19/2023] [Accepted: 10/27/2023] [Indexed: 11/22/2023] Open
Abstract
The animal germline lineage needs to be maintained along generations. However, some Caenorhabditis elegans wild isolates display a mortal germline phenotype, leading to sterility after several generations at 25°C. Using a genome-wide association approach, we detect a significant peak on chromosome III around 5 Mb, confirmed by introgressions. Thus, a seemingly deleterious genotype is maintained at intermediate frequency in the species. Environmental rescue is a likely explanation, and indeed associated bacteria and microsporidia suppress the phenotype of wild isolates as well as mutants in small RNA inheritance (nrde-2) and histone modifications (set-2). Escherichia coli strains of the K-12 lineage suppress the phenotype compared to B strains. By shifting a wild strain from E. coli K-12 to E. coli B, we find that memory of the suppressing condition is maintained over several generations. Thus, the mortal germline phenotype of wild C. elegans is in part revealed by laboratory conditions and may represent variation in epigenetic inheritance and environmental interactions. This study also points to the importance of non-genetic memory in the face of environmental variation.
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Affiliation(s)
- Lise Frézal
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Marie Saglio
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Gaotian Zhang
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Luke Noble
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Aurélien Richaud
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Marie-Anne Félix
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
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17
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Cheddadi R, Yeramilli V, Martin C. From Mother to Infant, from Placenta to Gut: Understanding Varied Microbiome Profiles in Neonates. Metabolites 2023; 13:1184. [PMID: 38132866 PMCID: PMC10745069 DOI: 10.3390/metabo13121184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
The field of human microbiome and gut microbial diversity research has witnessed a profound transformation, driven by advances in omics technologies. These advancements have unveiled essential connections between microbiome alterations and severe conditions, prompting the development of new frameworks through epidemiological studies. Traditionally, it was believed that each individual harbored unique microbial communities acquired early in life, evolving over the course of their lifetime, with little acknowledgment of any prenatal microbial development, but recent research challenges this belief. The neonatal microbiome's onset, influenced by factors like delivery mode and maternal health, remains a subject of intense debate, hinting at potential intrauterine microbial processes. In-depth research reveals associations between microbiome profiles and specific health outcomes, ranging from obesity to neurodevelopmental disorders. Understanding these diverse microbiome profiles is essential for unraveling the intricate relationships between the microbiome and health outcomes.
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Affiliation(s)
- Riadh Cheddadi
- Department of Surgery, Division of Pediatric Surgery, Washington University School of Medicine, Saint Louis, MO 63110, USA (C.M.)
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18
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Hiramatsu F, Lightfoot JW. Kin-recognition and predation shape collective behaviors in the cannibalistic nematode Pristionchus pacificus. PLoS Genet 2023; 19:e1011056. [PMID: 38096160 PMCID: PMC10721034 DOI: 10.1371/journal.pgen.1011056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/08/2023] [Indexed: 12/17/2023] Open
Abstract
Kin-recognition is observed across diverse species forming an important behavioral adaptation influencing organismal interactions. In many species, the molecular mechanisms involved are difficult to characterize, but in the nematode Pristionchus pacificus molecular components regulating its kin-recognition system have been identified. These determine its predatory behaviors towards other con-specifics which prevents the killing and cannibalization of kin. Importantly, their impact on other interactions including collective behaviors is unknown. Here, we explored a high altitude adapted clade of this species which aggregates abundantly under laboratory conditions, to investigate the influence of the kin-recognition system on their group behaviours. By utilizing pairwise aggregation assays between distinct strains of P. pacificus with differing degrees of genetic relatedness, we observe aggregation between kin but not distantly related strains. In assays between distantly related strains, the aggregation ratio is frequently reduced. Furthermore, abolishing predation behaviors through CRISPR/Cas9 induced mutations in Ppa-nhr-40 result in rival strains successfully aggregating together. Finally, as Caenorhabditis elegans are found naturally occurring with P. pacificus, we also explored aggregation events between these species. Here, aggregates were dominated by P. pacificus with the presence of only a small number of predators proving sufficient to disrupt C. elegans aggregation dynamics. Thus, aggregating strains of P. pacificus preferentially group with kin, revealing competition and nepotism as previously unknown components influencing collective behaviors in nematodes.
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Affiliation(s)
- Fumie Hiramatsu
- Max Planck Research Group Genetics of Behavior, Max Planck Institute for Neurobiology of Behavior–caesar, Bonn, Germany
- International Max Planck Research School for Brain and Behavior, Bonn, Germany
| | - James W. Lightfoot
- Max Planck Research Group Genetics of Behavior, Max Planck Institute for Neurobiology of Behavior–caesar, Bonn, Germany
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19
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Sepulveda NB, Chen D, Petrella LN. Moderate heat stress-induced sterility is due to motility defects and reduced mating drive in Caenorhabditis elegans males. J Exp Biol 2023; 226:jeb245546. [PMID: 37724024 DOI: 10.1242/jeb.245546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023]
Abstract
Moderate heat stress negatively impacts fertility in sexually reproducing organisms at sublethal temperatures. These moderate heat stress effects are typically more pronounced in males. In some species, sperm production, quality and motility are the primary cause of male infertility during moderate heat stress. However, this is not the case in the model nematode Caenorhabditis elegans, where changes in mating behavior are the primary cause of fertility loss. We report that heat-stressed C. elegans males are more motivated to locate and remain on food and less motivated to leave food to find and mate with hermaphrodites than their unstressed counterparts. Heat-stressed males also demonstrate a reduction in motility that likely limits their ability to mate. Collectively these changes result in a dramatic reduction in reproductive success. The reduction in mate-searching behavior may be partially due to increased expression of the chemoreceptor odr-10 in the AWA sensory neurons, which is a marker for starvation in males. These results demonstrate that moderate heat stress may have profound and previously underappreciated effects on reproductive behaviors. As climate change continues to raise global temperatures, it will be imperative to understand how moderate heat stress affects behavioral and motility elements critical to reproduction.
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Affiliation(s)
- Nicholas B Sepulveda
- Department of Biological Sciences, Marquette University, 1428 W Clybourn St., Milwaukee, WI 53217, USA
| | - Donald Chen
- Department of Biological Sciences, Marquette University, 1428 W Clybourn St., Milwaukee, WI 53217, USA
| | - Lisa N Petrella
- Department of Biological Sciences, Marquette University, 1428 W Clybourn St., Milwaukee, WI 53217, USA
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20
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Yeon J, Porwal C, McGrath PT, Sengupta P. Identification of a spontaneously arising variant affecting thermotaxis behavior in a recombinant inbred Caenorhabditis elegans line. G3 (BETHESDA, MD.) 2023; 13:jkad186. [PMID: 37572357 PMCID: PMC10542565 DOI: 10.1093/g3journal/jkad186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 06/26/2023] [Accepted: 08/02/2023] [Indexed: 08/14/2023]
Abstract
Analyses of the contributions of genetic variants in wild strains to phenotypic differences have led to a more complete description of the pathways underlying cellular functions. Causal loci are typically identified via interbreeding of strains with distinct phenotypes in order to establish recombinant inbred lines (RILs). Since the generation of RILs requires growth for multiple generations, their genomes may contain not only different combinations of parental alleles but also genetic changes that arose de novo during the establishment of these lines. Here, we report that in the course of generating RILs between Caenorhabditis elegans strains that exhibit distinct thermotaxis behavioral phenotypes, we identified spontaneously arising variants in the ttx-1 locus. ttx-1 encodes the terminal selector factor for the AFD thermosensory neurons, and loss-of-function mutations in ttx-1 abolish thermotaxis behaviors. The identified genetic changes in ttx-1 in the RIL are predicted to decrease ttx-1 function in part via specifically affecting a subset of AFD-expressed ttx-1 isoforms. Introduction of the relevant missense mutation in the laboratory C. elegans strain via gene editing recapitulates the thermotaxis behavioral defects of the RIL. Our results suggest that spontaneously occurring genomic changes in RILs may complicate identification of loci contributing to phenotypic variation, but that these mutations may nevertheless lead to the identification of important causal molecules and mechanisms.
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Affiliation(s)
- Jihye Yeon
- Department of Biology, Brandeis University, Waltham, MA 02454, USA
| | - Charmi Porwal
- Department of Biology, Brandeis University, Waltham, MA 02454, USA
| | - Patrick T McGrath
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Piali Sengupta
- Department of Biology, Brandeis University, Waltham, MA 02454, USA
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21
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Zhang X, Penkov S, Kurzchalia TV, Zaburdaev V. Periodic ethanol supply as a path toward unlimited lifespan of Caenorhabditis elegans dauer larvae. FRONTIERS IN AGING 2023; 4:1031161. [PMID: 37731965 PMCID: PMC10507685 DOI: 10.3389/fragi.2023.1031161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 08/14/2023] [Indexed: 09/22/2023]
Abstract
The dauer larva is a specialized stage of worm development optimized for survival under harsh conditions that have been used as a model for stress resistance, metabolic adaptations, and longevity. Recent findings suggest that the dauer larva of Caenorhabditis elegans may utilize external ethanol as an energy source to extend their lifespan. It was shown that while ethanol may serve as an effectively infinite source of energy, some toxic compounds accumulating as byproducts of its metabolism may lead to the damage of mitochondria and thus limit the lifespan of larvae. A minimal mathematical model was proposed to explain the connection between the lifespan of a dauer larva and its ethanol metabolism. To explore theoretically if it is possible to extend even further the lifespan of dauer larvae, we incorporated two natural mechanisms describing the recovery of damaged mitochondria and elimination of toxic compounds, which were previously omitted in the model. Numerical simulations of the revised model suggested that while the ethanol concentration is constant, the lifespan still stays limited. However, if ethanol is supplied periodically, with a suitable frequency and amplitude, the dauer could survive as long as we observe the system. Analytical methods further help to explain how feeding frequency and amplitude affect lifespan extension. Based on the comparison of the model with experimental data for fixed ethanol concentration, we proposed the range of feeding protocols that could lead to even longer dauer survival and it can be tested experimentally.
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Affiliation(s)
- Xingyu Zhang
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Sider Penkov
- Center of Membrane Biochemistry and Lipid Research, University Clinic and Faculty of Medicine, Dresden, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Clinic and Faculty of Medicine, Dresden, Germany
| | | | - Vasily Zaburdaev
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
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22
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Moya ND, Stevens L, Miller IR, Sokol CE, Galindo JL, Bardas AD, Koh ESH, Rozenich J, Yeo C, Xu M, Andersen EC. Novel and improved Caenorhabditis briggsae gene models generated by community curation. BMC Genomics 2023; 24:486. [PMID: 37626289 PMCID: PMC10463891 DOI: 10.1186/s12864-023-09582-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND The nematode Caenorhabditis briggsae has been used as a model in comparative genomics studies with Caenorhabditis elegans because of their striking morphological and behavioral similarities. However, the potential of C. briggsae for comparative studies is limited by the quality of its genome resources. The genome resources for the C. briggsae laboratory strain AF16 have not been developed to the same extent as C. elegans. The recent publication of a new chromosome-level reference genome for QX1410, a C. briggsae wild strain closely related to AF16, has provided the first step to bridge the gap between C. elegans and C. briggsae genome resources. Currently, the QX1410 gene models consist of software-derived gene predictions that contain numerous errors in their structure and coding sequences. In this study, a team of researchers manually inspected over 21,000 gene models and underlying transcriptomic data to repair software-derived errors. RESULTS We designed a detailed workflow to train a team of nine students to manually curate gene models using RNA read alignments. We manually inspected the gene models, proposed corrections to the coding sequences of over 8,000 genes, and modeled thousands of putative isoforms and untranslated regions. We exploited the conservation of protein sequence length between C. briggsae and C. elegans to quantify the improvement in protein-coding gene model quality and showed that manual curation led to substantial improvements in the protein sequence length accuracy of QX1410 genes. Additionally, collinear alignment analysis between the QX1410 and AF16 genomes revealed over 1,800 genes affected by spurious duplications and inversions in the AF16 genome that are now resolved in the QX1410 genome. CONCLUSIONS Community-based, manual curation using transcriptome data is an effective approach to improve the quality of software-derived protein-coding genes. The detailed protocols provided in this work can be useful for future large-scale manual curation projects in other species. Our manual curation efforts have brought the QX1410 gene models to a comparable level of quality as the extensively curated AF16 gene models. The improved genome resources for C. briggsae provide reliable tools for the study of Caenorhabditis biology and other related nematodes.
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Affiliation(s)
- Nicolas D Moya
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, 60208, USA
| | - Lewis Stevens
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Isabella R Miller
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Chloe E Sokol
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Joseph L Galindo
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Alexandra D Bardas
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Edward S H Koh
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Justine Rozenich
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Cassia Yeo
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Maryanne Xu
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA.
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23
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Martins AC, Virgolini MB, Ávila DS, Scharf P, Li J, Tinkov AA, Skalny AV, Bowman AB, Rocha JBT, Aschner M. Mitochondria in the Spotlight: C. elegans as a Model Organism to Evaluate Xenobiotic-Induced Dysfunction. Cells 2023; 12:2124. [PMID: 37681856 PMCID: PMC10486742 DOI: 10.3390/cells12172124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/19/2023] [Accepted: 08/20/2023] [Indexed: 09/09/2023] Open
Abstract
Mitochondria play a crucial role in cellular respiration, ATP production, and the regulation of various cellular processes. Mitochondrial dysfunctions have been directly linked to pathophysiological conditions, making them a significant target of interest in toxicological research. In recent years, there has been a growing need to understand the intricate effects of xenobiotics on human health, necessitating the use of effective scientific research tools. Caenorhabditis elegans (C. elegans), a nonpathogenic nematode, has emerged as a powerful tool for investigating toxic mechanisms and mitochondrial dysfunction. With remarkable genetic homology to mammals, C. elegans has been used in studies to elucidate the impact of contaminants and drugs on mitochondrial function. This review focuses on the effects of several toxic metals and metalloids, drugs of abuse and pesticides on mitochondria, highlighting the utility of C. elegans as a model organism to investigate mitochondrial dysfunction induced by xenobiotics. Mitochondrial structure, function, and dynamics are discussed, emphasizing their essential role in cellular viability and the regulation of processes such as autophagy, apoptosis, and calcium homeostasis. Additionally, specific toxins and toxicants, such as arsenic, cadmium, and manganese are examined in the context of their impact on mitochondrial function and the utility of C. elegans in elucidating the underlying mechanisms. Furthermore, we demonstrate the utilization of C. elegans as an experimental model providing a promising platform for investigating the intricate relationships between xenobiotics and mitochondrial dysfunction. This knowledge could contribute to the development of strategies to mitigate the adverse effects of contaminants and drugs of abuse, ultimately enhancing our understanding of these complex processes and promoting human health.
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Affiliation(s)
- Airton C. Martins
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
| | - Miriam B. Virgolini
- Departamento de Farmacología Otto Orsingher, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
- Instituto de Farmacología Experimental de Córdoba-Consejo Nacional de Investigaciones Técnicas (IFEC-CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Daiana Silva Ávila
- Laboratory of Biochemistry and Toxicology in Caenorhabditis Elegans, Universidade Federal do Pampa, Campus Uruguaiana, BR-472 Km 592, Uruguaiana 97500-970, RS, Brazil
| | - Pablo Scharf
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil
| | - Jung Li
- College of Osteopathic Medicine, Des Moines University, Des Moines, IA 50312, USA
| | - Alexey A. Tinkov
- Laboratory of Ecobiomonitoring and Quality Control, Yaroslavl State University, Yaroslavl 150003, Russia
- Laboratory of Molecular Dietetics, IM Sechenov First Moscow State Medical University (Sechenov University), Moscow 119435, Russia
| | - Anatoly V. Skalny
- Laboratory of Ecobiomonitoring and Quality Control, Yaroslavl State University, Yaroslavl 150003, Russia
- Laboratory of Molecular Dietetics, IM Sechenov First Moscow State Medical University (Sechenov University), Moscow 119435, Russia
- Peoples Friendship University of Russia (RUDN University), Moscow 117198, Russia
| | - Aaron B. Bowman
- School of Health Sciences, Purdue University, West Lafayette, IN 47907-2051, USA
| | - João B. T. Rocha
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
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Teterina AA, Willis JH, Lukac M, Jovelin R, Cutter AD, Phillips PC. Genomic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes. PLoS Genet 2023; 19:e1010879. [PMID: 37585484 PMCID: PMC10461856 DOI: 10.1371/journal.pgen.1010879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 08/28/2023] [Accepted: 07/21/2023] [Indexed: 08/18/2023] Open
Abstract
Caenorhabditis nematodes form an excellent model for studying how the mode of reproduction affects genetic diversity, as some species reproduce via outcrossing whereas others can self-fertilize. Currently, chromosome-level patterns of diversity and recombination are only available for self-reproducing Caenorhabditis, making the generality of genomic patterns across the genus unclear given the profound potential influence of reproductive mode. Here we present a whole-genome diversity landscape, coupled with a new genetic map, for the outcrossing nematode C. remanei. We demonstrate that the genomic distribution of recombination in C. remanei, like the model nematode C. elegans, shows high recombination rates on chromosome arms and low rates toward the central regions. Patterns of genetic variation across the genome are also similar between these species, but differ dramatically in scale, being tenfold greater for C. remanei. Historical reconstructions of variation in effective population size over the past million generations echo this difference in polymorphism. Evolutionary simulations demonstrate how selection, recombination, mutation, and selfing shape variation along the genome, and that multiple drivers can produce patterns similar to those observed in natural populations. The results illustrate how genome organization and selection play a crucial role in shaping the genomic pattern of diversity whereas demographic processes scale the level of diversity across the genome as a whole.
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Affiliation(s)
- Anastasia A. Teterina
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
- Center of Parasitology, Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | - John H. Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Matt Lukac
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Richard Jovelin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Asher D. Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Patrick C. Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
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Moya ND, Stevens L, Miller IR, Sokol CE, Galindo JL, Bardas AD, Koh ESH, Rozenich J, Yeo C, Xu M, Andersen EC. Novel and improved Caenorhabditis briggsae gene models generated by community curation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541014. [PMID: 37292880 PMCID: PMC10245686 DOI: 10.1101/2023.05.16.541014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Background The nematode Caenorhabditis briggsae has been used as a model for genomics studies compared to Caenorhabditis elegans because of its striking morphological and behavioral similarities. These studies yielded numerous findings that have expanded our understanding of nematode development and evolution. However, the potential of C. briggsae to study nematode biology is limited by the quality of its genome resources. The reference genome and gene models for the C. briggsae laboratory strain AF16 have not been developed to the same extent as C. elegans . The recent publication of a new chromosome-level reference genome for QX1410, a C. briggsae wild strain closely related to AF16, has provided the first step to bridge the gap between C. elegans and C. briggsae genome resources. Currently, the QX1410 gene models consist of protein-coding gene predictions generated from short- and long-read transcriptomic data. Because of the limitations of gene prediction software, the existing gene models for QX1410 contain numerous errors in their structure and coding sequences. In this study, a team of researchers manually inspected over 21,000 software-derived gene models and underlying transcriptomic data to improve the protein-coding gene models of the C. briggsae QX1410 genome. Results We designed a detailed workflow to train a team of nine students to manually curate genes using RNA read alignments and predicted gene models. We manually inspected the gene models using the genome annotation editor, Apollo, and proposed corrections to the coding sequences of over 8,000 genes. Additionally, we modeled thousands of putative isoforms and untranslated regions. We exploited the conservation of protein sequence length between C. briggsae and C. elegans to quantify the improvement in protein-coding gene model quality before and after curation. Manual curation led to a substantial improvement in the protein sequence length accuracy of QX1410 genes. We also compared the curated QX1410 gene models against the existing AF16 gene models. The manual curation efforts yielded QX1410 gene models that are similar in quality to the extensively curated AF16 gene models in terms of protein-length accuracy and biological completeness scores. Collinear alignment analysis between the QX1410 and AF16 genomes revealed over 1,800 genes affected by spurious duplications and inversions in the AF16 genome that are now resolved in the QX1410 genome. Conclusions Community-based, manual curation using transcriptome data is an effective approach to improve the quality of software-derived protein-coding genes. Comparative genomic analysis using a related species with high-quality reference genome(s) and gene models can be used to quantify improvements in gene model quality in a newly sequenced genome. The detailed protocols provided in this work can be useful for future large-scale manual curation projects in other species. The chromosome-level reference genome for the C. briggsae strain QX1410 far surpasses the quality of the genome of the laboratory strain AF16, and our manual curation efforts have brought the QX1410 gene models to a comparable level of quality to the previous reference, AF16. The improved genome resources for C. briggsae provide reliable tools for the study of Caenorhabditis biology and other related nematodes.
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Affiliation(s)
- Nicolas D. Moya
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
| | - Lewis Stevens
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Isabella R. Miller
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Chloe E. Sokol
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Joseph L. Galindo
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Alexandra D. Bardas
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Edward S. H. Koh
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Justine Rozenich
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Cassia Yeo
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Maryanne Xu
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Erik C. Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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Luo J, Barrios A, Portman DS. C. elegans males optimize mate-choice decisions via sex-specific responses to multimodal sensory cues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.08.536021. [PMID: 37066192 PMCID: PMC10104232 DOI: 10.1101/2023.04.08.536021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
For sexually reproducing animals, selecting optimal mates is essential for maximizing reproductive fitness. Because the nematode C. elegans reproduces mostly by self-fertilization, little is known about its mate-choice behaviors. While several sensory cues have been implicated in males' ability to recognize hermaphrodites, achieving an integrated understanding of the ways males use these cues to assess relevant characteristics of potential mates has proven challenging. Here, we use a choice-based social-interaction assay to explore the ability of C. elegans males to make and optimize mate choices. We find that males use a combination of volatile sex pheromones (VSPs), ascaroside pheromones, surface-bound chemical cues, and other signals to robustly assess a variety of features of potential mates. Specific aspects of mate choice are communicated by distinct signals: the presence of a sperm-depleted, receptive hermaphrodite is likely signaled by VSPs, while developmental stage and sex are redundantly specified by ascaroside pheromones and surface-associated cues. Ascarosides also signal nutritional information, allowing males to choose well-fed over starved mates, while both ascarosides and surface-associated cues cause males to prefer virgin over previously mated hermaphrodites. The male-specificity of these behavioral responses is determined by both male-specific neurons and the male state of sex-shared circuits, and we reveal an unexpected role for the sex-shared ASH sensory neurons in male attraction to endogenously produced hermaphrodite ascarosides. Together, our findings lead to an integrated view of the signaling and behavioral mechanisms by which males use diverse sensory cues to assess multiple features of potential mates and optimize mate choice.
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Affiliation(s)
- Jintao Luo
- School of Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China
- Department of Biomedical Genetics and Del Monte Institute for Neuroscience, University of Rochester, Rochester, NY 14642
| | - Arantza Barrios
- Department of Cell and Developmental Biology, University College London, London WC1E 6DE, UK
| | - Douglas S. Portman
- Department of Biomedical Genetics and Del Monte Institute for Neuroscience, University of Rochester, Rochester, NY 14642
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Petersen C, Krahn A, Leippe M. The nematode Caenorhabditis elegans and diverse potential invertebrate vectors predominantly interact opportunistically. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1069056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Some small animals migrate with the help of other, more mobile animals (phoresy) to leave short-lived and resource-poor habitats. The nematode Caenorhabditis elegans lives in ephemeral habitats such as compost, but has also been found associated with various potential invertebrate vectors. Little research has been done to determine if C. elegans is directly attracted to these invertebrates. To determine whether C. elegans is attracted to compounds and volatile odorants of invertebrates, we conducted chemotaxis experiments with the isopods Porcellio scaber, Oniscus asellus, and Armadillidium sp. and with Lithobius sp. myriapods, Drosophila melanogaster fruit flies, and Arion sp. slugs as representatives of natural vectors. Because phoresy is an important escape strategy in nature, especially for dauer larvae of C. elegans, we examined the attraction of the natural C. elegans isolate MY2079 in addition to the laboratory-adapted strain N2 at the dauer and L4 stage. We found that DMSO washing solution of Lithobius sp. and the odor of live D. melanogaster attracted C. elegans N2 L4 larvae. Surprisingly, the natural isolate MY2079 was not attracted to any invertebrate during either the dauer or L4 life stages and both C. elegans strains were repelled by various compounds from O. asellus, P. scaber, Armadillidium sp., Lithobius sp., and Arion sp. feces. We hypothesize that this is due to defense chemicals released by the invertebrates. Although compounds from Lithobius sp. and D. melanogaster odorants were mildly attractive, the lack of attraction to most invertebrates suggests a predominantly opportunistic association between C. elegans and invertebrate vectors.
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Wan YC, Troemel ER, Reinke AW. Conservation of Nematocida microsporidia gene expression and host response in Caenorhabditis nematodes. PLoS One 2022; 17:e0279103. [PMID: 36534656 PMCID: PMC9762603 DOI: 10.1371/journal.pone.0279103] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Microsporidia are obligate intracellular parasites that are known to infect most types of animals. Many species of microsporidia can infect multiple related hosts, but it is not known if microsporidia express different genes depending upon which host species is infected or if the host response to infection is specific to each microsporidia species. To address these questions, we took advantage of two species of Nematocida microsporidia, N. parisii and N. ausubeli, that infect two species of Caenorhabditis nematodes, C. elegans and C. briggsae. We performed RNA-seq at several time points for each host infected with either microsporidia species. We observed that Nematocida transcription was largely independent of its host. We also observed that the host transcriptional response was similar when infected with either microsporidia species. Finally, we analyzed if the host response to microsporidia infection was conserved across host species. We observed that although many of the genes upregulated in response to infection are not direct orthologs, the same expanded gene families are upregulated in both Caenorhabditis hosts. Together our results describe the transcriptional interactions of Nematocida infection in Caenorhabditis hosts and demonstrate that these responses are evolutionarily conserved.
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Affiliation(s)
- Yin Chen Wan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Emily R. Troemel
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Aaron W. Reinke
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada,* E-mail:
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Preusser F, Neuschulz A, Junker JP, Rajewsky N, Preibisch S. Long-term imaging reveals behavioral plasticity during C. elegans dauer exit. BMC Biol 2022; 20:277. [PMID: 36514066 DOI: 10.1186/s12915-022-01471-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND During their lifetime, animals must adapt their behavior to survive in changing environments. This ability requires the nervous system to undergo adjustments at distinct temporal scales, from short-term dynamic changes in expression of neurotransmitters and receptors to longer-term growth, spatial and connectivity reorganization, while integrating external stimuli. The nematode Caenorhabditis elegans provides a model of nervous system plasticity, in particular its dauer exit decision. Under unfavorable conditions, larvae will enter the non-feeding and non-reproductive stress-resistant dauer stage and adapt their behavior to cope with the harsh new environment, with active reversal under improved conditions leading to resumption of reproductive development. However, how different environmental stimuli regulate the exit decision mechanism and thereby drive the larva's behavioral change is unknown. To fill this gap and provide insights on behavioral changes over extended periods of time, we developed a new open hardware method for long-term imaging (12h) of C. elegans larvae. RESULTS Our WormObserver platform comprises open hardware and software components for video acquisition, automated processing of large image data (> 80k images/experiment) and data analysis. We identified dauer-specific behavioral motifs and characterized the behavioral trajectory of dauer exit in different environments and genetic backgrounds to identify key decision points and stimuli promoting dauer exit. Combining long-term behavioral imaging with transcriptomics data, we find that bacterial ingestion triggers a change in neuropeptide gene expression to establish post-dauer behavior. CONCLUSIONS Taken together, we show how a developing nervous system can robustly integrate environmental changes activate a developmental switch and adapt the organism's behavior to a new environment. WormObserver is generally applicable to other research questions within and beyond the C. elegans field, having a modular and customizable character and allowing assessment of behavioral plasticity over longer periods.
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Affiliation(s)
- Friedrich Preusser
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany. .,Institute for Biology, Humboldt University of Berlin, 10099, Berlin, Germany.
| | - Anika Neuschulz
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany.,Institute for Biology, Humboldt University of Berlin, 10099, Berlin, Germany
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
| | - Stephan Preibisch
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA.
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30
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The Thermal Stress Coping Network of the Nematode Caenorhabditis elegans. Int J Mol Sci 2022; 23:ijms232314907. [PMID: 36499234 PMCID: PMC9737000 DOI: 10.3390/ijms232314907] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/11/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022] Open
Abstract
Response to hyperthermia, highly conserved from bacteria to humans, involves transcriptional upregulation of genes involved in battling the cytotoxicity caused by misfolded and denatured proteins, with the aim of proteostasis restoration. C. elegans senses and responds to changes in growth temperature or noxious thermal stress by well-defined signaling pathways. Under adverse conditions, regulation of the heat shock response (HSR) in C. elegans is controlled by a single transcription factor, heat-shock factor 1 (HSF-1). HSR and HSF-1 in particular are proven to be central to survival under proteotoxic stress, with additional roles in normal physiological processes. For years, it was a common belief that upregulation of heat shock proteins (HSPs) by HSF-1 was the main and most important step toward thermotolerance. However, an ever-growing number of studies have shown that targets of HSF-1 involved in cytoskeletal and exoskeletal integrity preservation as well as other HSF-1 dependent and independent pathways are equally important. In this review, we follow the thermal stimulus from reception by the nematode nerve endings till the activation of cellular response programs. We analyze the different HSF-1 functions in HSR as well as all the recently discovered mechanisms that add to the knowledge of the heat stress coping network of C. elegans.
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31
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Yoon KH, Indong RA, Lee JI. Making "Sense" of Ecology from a Genetic Perspective: Caenorhabditis elegans, Microbes and Behavior. Metabolites 2022; 12:1084. [PMID: 36355167 PMCID: PMC9697003 DOI: 10.3390/metabo12111084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/02/2022] [Accepted: 11/05/2022] [Indexed: 12/31/2023] Open
Abstract
Our knowledge of animal and behavior in the natural ecology is based on over a century's worth of valuable field studies. In this post-genome era, however, we recognize that genes are the underpinning of ecological interactions between two organisms. Understanding how genes contribute to animal ecology, which is essentially the intersection of two genomes, is a tremendous challenge. The bacterivorous nematode Caenorhabditis elegans, one of the most well-known genetic animal model experimental systems, experiences a complex microbial world in its natural habitat, providing us with a window into the interplay of genes and molecules that result in an animal-microbial ecology. In this review, we will discuss C. elegans natural ecology, how the worm uses its sensory system to detect the microbes and metabolites that it encounters, and then discuss some of the fascinating ecological dances, including behaviors, that have evolved between the nematode and the microbes in its environment.
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Affiliation(s)
- Kyoung-hye Yoon
- Department of Physiology, Mitohormesis Research Center, Yonsei University Wonju College of Medicine, Wonju 26426, Korea
| | - Rocel Amor Indong
- Division of Biological Science and Technology, College of Science and Technology, Yonsei University, Wonju 26493, Korea
| | - Jin I. Lee
- Division of Biological Science and Technology, College of Science and Technology, Yonsei University, Wonju 26493, Korea
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32
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Geng S, Li Q, Zhou X, Zheng J, Liu H, Zeng J, Yang R, Fu H, Hao F, Feng Q, Qi B. Gut commensal E. coli outer membrane proteins activate the host food digestive system through neural-immune communication. Cell Host Microbe 2022; 30:1401-1416.e8. [PMID: 36057258 DOI: 10.1016/j.chom.2022.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/01/2022] [Accepted: 08/05/2022] [Indexed: 12/13/2022]
Abstract
The gastrointestinal tract facilitates food digestion, with the gut microbiota playing pivotal roles in nutrient breakdown and absorption. However, the microbial molecules and downstream signaling pathways that activate food digestion remain unexplored. Here, by establishing a food digestion system in C. elegans, we discover that food breakdown is regulated by the interaction between bacterial outer membrane proteins (OMPs) and a neural-immune pathway. E. coli OmpF/A activate digestion by increasing the neuropeptide NLP-12 that acts on the receptor CCKR. NLP-12 is homologous to mammalian cholecystokinin, known to stimulate dopamine, and we found that loss of dopamine receptors or addition of a dopamine antagonist inhibited OMP-mediated digestion. Dopamine and NLP-12-CKR-1 converge to inhibit PMK-1/p38 innate immune signaling. Moreover, directly inhibiting PMK-1/p38 boosts food digestion. This study uncovers a role of bacterial OMPs in regulating animal nutrient uptake and supports a key role for innate immunity in digestion.
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Affiliation(s)
- Shengya Geng
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Qian Li
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Xue Zhou
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Junkang Zheng
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Huimin Liu
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Jie Zeng
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Ruizhi Yang
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Herui Fu
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Fanrui Hao
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Qianxu Feng
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Bin Qi
- Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China.
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Wang Y, Guo K, Wang Q, Zhong G, Zhang W, Jiang Y, Mao X, Li X, Huang Z. Caenorhabditis elegans as an emerging model in food and nutrition research: importance of standardizing base diet. Crit Rev Food Sci Nutr 2022; 64:3167-3185. [PMID: 36200941 DOI: 10.1080/10408398.2022.2130875] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
As a model organism that has helped revolutionize life sciences, Caenorhabditis elegans has been increasingly used in nutrition research. Here we explore the tradeoffs between pros and cons of its use as a dietary model based primarily on literature review from the past decade. We first provide an overview of its experimental strengths as an animal model, focusing on lifespan and healthspan, behavioral and physiological phenotypes, and conservation of key nutritional pathways. We then summarize recent advances of its use in nutritional studies, e.g. food preference and feeding behavior, sugar status and metabolic reprogramming, lifetime and transgenerational nutrition tracking, and diet-microbiota-host interactions, highlighting cutting-edge technologies originated from or developed in C. elegans. We further review current challenges of using C. elegans as a nutritional model, followed by in-depth discussions on potential solutions. In particular, growth scales and throughputs, food uptake mode, and axenic culture of C. elegans are appraised in the context of food research. We also provide perspectives for future development of chemically defined nematode food ("NemaFood") for C. elegans, which is now widely accepted as a versatile and affordable in vivo model and has begun to show transformative potential to pioneer nutrition science.
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Affiliation(s)
- Yuqing Wang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
| | - Kaixin Guo
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Qiangqiang Wang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
| | - Guohuan Zhong
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Center for Bioresources and Drug Discovery, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Wenjun Zhang
- Center for Bioresources and Drug Discovery, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yiyi Jiang
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
- Perfect Life & Health Institute, Zhongshan, Guangdong, China
| | - Xinliang Mao
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
- Perfect Life & Health Institute, Zhongshan, Guangdong, China
| | - Xiaomin Li
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
- Perfect Life & Health Institute, Zhongshan, Guangdong, China
| | - Zebo Huang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
- Center for Bioresources and Drug Discovery, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
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Shaw CL, Kennedy DA. Developing an empirical model for spillover and emergence: Orsay virus host range in Caenorhabditis. Proc Biol Sci 2022; 289:20221165. [PMID: 36126684 PMCID: PMC9489279 DOI: 10.1098/rspb.2022.1165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/24/2022] [Indexed: 11/20/2022] Open
Abstract
A lack of tractable experimental systems in which to test hypotheses about the ecological and evolutionary drivers of disease spillover and emergence has limited our understanding of these processes. Here we introduce a promising system: Caenorhabditis hosts and Orsay virus, a positive-sense single-stranded RNA virus that naturally infects C. elegans. We assayed species across the Caenorhabditis tree and found Orsay virus susceptibility in 21 of 84 wild strains belonging to 14 of 44 species. Confirming patterns documented in other systems, we detected effects of host phylogeny on susceptibility. We then tested whether susceptible strains were capable of transmitting Orsay virus by transplanting exposed hosts and determining whether they transmitted infection to conspecifics during serial passage. We found no evidence of transmission in 10 strains (virus undetectable after passaging in all replicates), evidence of low-level transmission in 5 strains (virus lost between passage 1 and 5 in at least one replicate) and evidence of sustained transmission in 6 strains (including all three experimental C. elegans strains) in at least one replicate. Transmission was strongly associated with viral amplification in exposed populations. Variation in Orsay virus susceptibility and transmission among Caenorhabditis strains suggests that the system could be powerful for studying spillover and emergence.
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Affiliation(s)
- Clara L. Shaw
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - David A. Kennedy
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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The p38 MAPK/PMK-1 Pathway Is Required for Resistance to Nocardia farcinica Infection in Caenorhabditis elegance. Pathogens 2022; 11:pathogens11101071. [PMID: 36297128 PMCID: PMC9609018 DOI: 10.3390/pathogens11101071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 12/02/2022] Open
Abstract
Nocardia farcinica is an opportunistic pathogen that causes nocardiosis primarily in patients with compromised immune systems. In this study, we used the genetically tractable organism Caenorhabditis elegans as a model to study the innate immune responses to N. farcinica infection. We found that unlike other pathogenic bacteria such as Pseudomonas aeruginosa and Staphylococcus aureus, N. farcinica failed to kill adult worms. In another words, adult worms exposed to N. farcinica exhibited a normal lifespan, compared with those fed the standard laboratory food bacterium Escherichia coli OP50. Interestingly, deletion of three core genes (pmk-1, nsy-1 and sek-1) in the p38 MAPK/PMK-1 pathway reduced the survival of worm exposure to N. farcinica, highlighting a crucial role of this pathway for C. elegans in resistance to N. farcinica. Furthermore, our results revealed that N. farcinica exposure up-regulated the level of PMK-1 phosphorylation. The activation of PMK-1 promoted nuclear translocation of a transcription factor SKN-1/Nrf2, which in turn mediated N. farcinica infection resistance in C. elegans. Our results provide an excellent example that the integrity of immune system is key aspect for counteract with pathogenesis of N. farcinica.
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Salas A, Rusconi JM, Rocca M, Lucas FD, Balcazar D, Achinelly MF. A new wild strain of Caenorhabditis elegans associated with Allograpta exotica (Syrphidae) in Argentina: an update of its ecological niche and worldwide distribution. AN ACAD BRAS CIENC 2022; 94:e20201440. [PMID: 35920483 DOI: 10.1590/0001-3765202220201440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 09/06/2021] [Indexed: 11/21/2022] Open
Abstract
Caenorhabditis elegans is a free-living nematode, belonging to the bacterivorous trophic group. Although it was cited in several countries, in different types of ecosystems and in associations with other organisms, the wild habitats of this nematode have not yet been precisely defined. In Argentina, C. elegans was recently isolated from the hoverfly Allograpta exotica, a voracious predator with potential biological control against aphids in horticultural crops. In this frame, the objectives of this study were (i) to characterize it molecularly and morphologically (ii) to report a wild strain of C. elegans for the first time from Argentina, (iii) to present a new ecological niche by associating it with A. exotica and (iv) to evaluate the pathogenicity against these insects. The results of the morphological and molecular analyses made it possible to determine that the isolated nematode was C. elegans, thus establishing the ARGLP1900 wild strain as the first record of this nematode for Argentina. A new association was described, since there are no records of interaction between C. elegans and A. exotica, providing information on a new ecological niche. The new wild strain found in this work, could be appropriate for comparative genomic studies with other C. elegans strains.
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Affiliation(s)
- Augusto Salas
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola, L de la Torre, s/n, G lvez, G lvez, Argentina
| | - José M Rusconi
- Centro de Estudios Parasitológicos y de Vectores CEPAVE (CCT La Plata, CONICET/UNLP), Blvd. 120 1900, La Plata, Provincia de Buenos Aires, Argentina
| | - Margarita Rocca
- Centro de Estudios Parasitológicos y de Vectores CEPAVE (CCT La Plata, CONICET/UNLP), Blvd. 120 1900, La Plata, Provincia de Buenos Aires, Argentina
| | - Florencia D Lucas
- Centro de Estudios Parasitológicos y de Vectores CEPAVE (CCT La Plata, CONICET/UNLP), Blvd. 120 1900, La Plata, Provincia de Buenos Aires, Argentina
| | - Darío Balcazar
- Centro de Estudios Parasitológicos y de Vectores CEPAVE (CCT La Plata, CONICET/UNLP), Blvd. 120 1900, La Plata, Provincia de Buenos Aires, Argentina
| | - María Fernanda Achinelly
- Centro de Estudios Parasitológicos y de Vectores CEPAVE (CCT La Plata, CONICET/UNLP), Blvd. 120 1900, La Plata, Provincia de Buenos Aires, Argentina
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Lazaro-Pena MI, Ward ZC, Yang S, Strohm A, Merrill AK, Soto CA, Samuelson AV. HSF-1: Guardian of the Proteome Through Integration of Longevity Signals to the Proteostatic Network. FRONTIERS IN AGING 2022; 3:861686. [PMID: 35874276 PMCID: PMC9304931 DOI: 10.3389/fragi.2022.861686] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/13/2022] [Indexed: 12/15/2022]
Abstract
Discoveries made in the nematode Caenorhabditis elegans revealed that aging is under genetic control. Since these transformative initial studies, C. elegans has become a premier model system for aging research. Critically, the genes, pathways, and processes that have fundamental roles in organismal aging are deeply conserved throughout evolution. This conservation has led to a wealth of knowledge regarding both the processes that influence aging and the identification of molecular and cellular hallmarks that play a causative role in the physiological decline of organisms. One key feature of age-associated decline is the failure of mechanisms that maintain proper function of the proteome (proteostasis). Here we highlight components of the proteostatic network that act to maintain the proteome and how this network integrates into major longevity signaling pathways. We focus in depth on the heat shock transcription factor 1 (HSF1), the central regulator of gene expression for proteins that maintain the cytosolic and nuclear proteomes, and a key effector of longevity signals.
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Affiliation(s)
- Maria I. Lazaro-Pena
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, United States
| | - Zachary C. Ward
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, United States
| | - Sifan Yang
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, United States
- Department of Biology, University of Rochester, Rochester, NY, United States
| | - Alexandra Strohm
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, United States
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, United States
- Toxicology Training Program, University of Rochester Medical Center, Rochester, NY, United States
| | - Alyssa K. Merrill
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, United States
- Toxicology Training Program, University of Rochester Medical Center, Rochester, NY, United States
| | - Celia A. Soto
- Department of Pathology, University of Rochester Medical Center, Rochester, NY, United States
- Cell Biology of Disease Graduate Program, University of Rochester Medical Center, Rochester, NY, United States
| | - Andrew V. Samuelson
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, United States
- *Correspondence: Andrew V. Samuelson,
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Sloat SA, Noble LM, Paaby AB, Bernstein M, Chang A, Kaur T, Yuen J, Tintori SC, Jackson JL, Martel A, Salome Correa JA, Stevens L, Kiontke K, Blaxter M, Rockman MV. Caenorhabditis nematodes colonize ephemeral resource patches in neotropical forests. Ecol Evol 2022; 12:e9124. [PMID: 35898425 PMCID: PMC9309040 DOI: 10.1002/ece3.9124] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/17/2022] [Accepted: 06/23/2022] [Indexed: 01/09/2023] Open
Abstract
Factors shaping the distribution and abundance of species include life-history traits, population structure, and stochastic colonization-extinction dynamics. Field studies of model species groups help reveal the roles of these factors. Species of Caenorhabditis nematodes are highly divergent at the sequence level but exhibit highly conserved morphology, and many of these species live in sympatry on microbe-rich patches of rotten material. Here, we use field experiments and large-scale opportunistic collections to investigate species composition, abundance, and colonization efficiency of Caenorhabditis species in two of the world's best-studied lowland tropical field sites: Barro Colorado Island in Panamá and La Selva in Sarapiquí, Costa Rica. We observed seven species of Caenorhabditis, four of them known only from these collections. We formally describe two species and place them within the Caenorhabditis phylogeny. While these localities contain species from many parts of the phylogeny, both localities were dominated by globally distributed androdiecious species. We found that Caenorhabditis individuals were able to colonize baits accessible only through phoresy and preferentially colonized baits that were in direct contact with the ground. We estimate the number of colonization events per patch to be low.
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Affiliation(s)
- Solomon A. Sloat
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Luke M. Noble
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Annalise B. Paaby
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaGeorgiaUSA
| | - Max Bernstein
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Audrey Chang
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Taniya Kaur
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - John Yuen
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
- Renaissance School of MedicineStony Brook UniversityStony BrookNew YorkUSA
| | - Sophia C. Tintori
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Jacqueline L. Jackson
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Arielle Martel
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Jose A. Salome Correa
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | | | - Karin Kiontke
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger InstituteHinxtonUK
| | - Matthew V. Rockman
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
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Bubrig LT, Janisch AN, Tillet EM, Gibson AK. Contrasting parasite-mediated reductions in fitness within versus between patches of a nematode host. Evolution 2022; 76:1556-1564. [PMID: 35652582 PMCID: PMC9329228 DOI: 10.1111/evo.14521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/22/2022] [Accepted: 03/28/2022] [Indexed: 01/22/2023]
Abstract
Host and parasites interact across spatial scales, but parasite-mediated fitness effects are typically measured only at local scales. Recent work suggests that parasites can reduce host fitness during dispersal between patches, highlighting the potential for both within- and between-patch effects to contribute to the net fitness consequences of parasitism. Building on this work, we measured the contribution of the dispersal phase to parasite-mediated reductions in host fitness. We used the nematode Caenorhabditis elegans and its natural microsporidian parasite Nematocida parisii to quantify the fitness consequences of parasitism at the individual, population, and metapopulation level. Nematocida parisii reduced individual fecundity and population growth but had its greatest fitness impact at the dispersal stage: parasitism reduced the fitness of dispersing larvae by 62%-100%. These results indicate that the cost of parasitism in this system is greatly underestimated if the metapopulation level is not taken into account. We also found that the effects of N. parisii vary with host genotype, and the relative advantage of the most resistant genotype increases with inclusion of the dispersal stage. Taken together, our findings demonstrate that host-parasite interactions at the dispersal stage can magnify selection for parasite resistance.
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Affiliation(s)
- Louis T. Bubrig
- Department of BiologyUniversity of VirginiaCharlottesvilleVirginia22904
| | - Anne N. Janisch
- Department of BiologyUniversity of VirginiaCharlottesvilleVirginia22904
| | - Emily M. Tillet
- Department of BiologyUniversity of VirginiaCharlottesvilleVirginia22904
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40
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Soil Nematodes as the Silent Sufferers of Climate-Induced Toxicity: Analysing the Outcomes of Their Interactions with Climatic Stress Factors on Land Cover and Agricultural Production. Appl Biochem Biotechnol 2022; 195:2519-2586. [PMID: 35593954 DOI: 10.1007/s12010-022-03965-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/10/2022] [Indexed: 11/02/2022]
Abstract
Unsustainable anthropogenic activities over the last few decades have resulted in alterations of the global climate. It can be perceived through changes in the rainfall patterns and rise in mean annual temperatures. Climatic stress factors exert their effects on soil health mainly by modifying the soil microenvironments where the soil fauna reside. Among the members of soil fauna, the soil nematodes have been found to be sensitive to these stress factors primarily because of their low tolerance limits. Additionally, because of their higher and diverse trophic positions in the soil food web they can integrate the effects of many stress factors acting together. This is important because under natural conditions the climatic stress factors do not exert their effect individually. Rather, they interact amongst themselves and other abiotic stress factors in the soil to generate their impacts. Some of these interactions may be synergistic while others may be antagonistic. As such, it becomes very difficult to assess their impacts on soil health by simply analysing the physicochemical properties of soil. This makes soil nematodes outstanding candidates for studying the effects of climatic stress factors on soil biology. The knowledge obtained therefrom can be used to design sustainable agricultural practices because most of the conventional techniques aim at short-term benefits with complete disregard of soil biology. This can partly ensure food security in the coming decades for the expanding population. Moreover, understanding soil biology can help to preserve landscapes that have developed over long periods of climatic stability and belowground soil biota interactions.
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41
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Saber S, Snyder M, Rajaei M, Baer CF. Mutation, selection, and the prevalence of the Caenorhabditis elegans heat-sensitive mortal germline phenotype. G3 (BETHESDA, MD.) 2022; 12:jkac063. [PMID: 35311992 PMCID: PMC9073675 DOI: 10.1093/g3journal/jkac063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/10/2022] [Indexed: 11/17/2022]
Abstract
Caenorhabditis elegans strains with the heat-sensitive mortal germline phenotype become progressively sterile over the course of a few tens of generations when maintained at temperatures near the upper range of C. elegans' tolerance. Mortal germline is transgenerationally heritable, and proximately under epigenetic control. Previous studies have suggested that mortal germline presents a relatively large mutational target and that mortal germline is not uncommon in natural populations of C. elegans. The mortal germline phenotype is not monolithic. Some strains exhibit a strong mortal germline phenotype, in which individuals invariably become sterile over a few generations, whereas other strains show a weaker (less penetrant) phenotype in which the onset of sterility is slower and more stochastic. We present results in which we (1) quantify the rate of mutation to the mortal germline phenotype and (2) quantify the frequency of mortal germline in a collection of 95 wild isolates. Over the course of ∼16,000 meioses, we detected one mutation to a strong mortal germline phenotype, resulting in a point estimate of the mutation rate UMrt≈ 6×10-5/genome/generation. We detected no mutations to a weak mortal germline phenotype. Six out of 95 wild isolates have a strong mortal germline phenotype, and although quantification of the weak mortal germline phenotype is inexact, the weak mortal germline phenotype is not rare in nature. We estimate a strength of selection against mutations conferring the strong mortal germline phenotype s¯≈0.1%, similar to selection against mutations affecting competitive fitness. The appreciable frequency of weak mortal germline variants in nature combined with the low mutation rate suggests that mortal germline may be maintained by balancing selection.
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Affiliation(s)
- Sayran Saber
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
| | - Michael Snyder
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
| | - Moein Rajaei
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
| | - Charles F Baer
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
- University of Florida Genetics Institute, Gainesville, FL 32610, USA
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42
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Stevens L, Moya ND, Tanny RE, Gibson SB, Tracey A, Na H, Chitrakar R, Dekker J, Walhout AJ, Baugh LR, Andersen EC. Chromosome-level reference genomes for two strains of Caenorhabditis briggsae: an improved platform for comparative genomics. Genome Biol Evol 2022; 14:6554914. [PMID: 35348662 PMCID: PMC9011032 DOI: 10.1093/gbe/evac042] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
The publication of the Caenorhabditis briggsae reference genome in 2003 enabled the first comparative genomics studies between C. elegans and C. briggsae, shedding light on the evolution of genome content and structure in the Caenorhabditis genus. However, despite being widely used, the currently available C. briggsae reference genome is substantially less complete and structurally accurate than the C. elegans reference genome. Here, we used high-coverage Oxford Nanopore long-read and chromosome conformation capture data to generate chromosome-level reference genomes for two C. briggsae strains: QX1410, a new reference strain closely related to the laboratory AF16 strain, and VX34, a highly divergent strain isolated in China. We also sequenced 99 recombinant inbred lines (RILs) generated from reciprocal crosses between QX1410 and VX34 to create a recombination map and identify chromosomal domains. Additionally, we used both short- and long-read RNA sequencing (RNA-seq) data to generate high-quality gene annotations. By comparing these new reference genomes to the current reference, we reveal that hyper-divergent haplotypes cover large portions of the C. briggsae genome, similar to recent reports in C. elegans and C. tropicalis. We also show that the genomes of selfing Caenorhabditis species have undergone more rearrangement than their outcrossing relatives, which has biased previous estimates of rearrangement rate in Caenorhabditis. These new genomes provide a substantially improved platform for comparative genomics in Caenorhabditis and narrow the gap between the quality of genomic resources available for C. elegans and C. briggsae.
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Affiliation(s)
- Lewis Stevens
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Nicolas D. Moya
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
| | - Robyn E. Tanny
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Sophia B. Gibson
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Huimin Na
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Albertha J.M. Walhout
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - L. Ryan Baugh
- Department of Biology, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Erik C. Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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Cohen SM, Wrobel CJJ, Prakash SJ, Schroeder FC, Sternberg PW. Formation and function of dauer ascarosides in the nematodes Caenorhabditis briggsae and Caenorhabditis elegans. G3 GENES|GENOMES|GENETICS 2022; 12:6517505. [PMID: 35094091 PMCID: PMC8895998 DOI: 10.1093/g3journal/jkac014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/22/2021] [Indexed: 11/12/2022]
Abstract
Abstract
The biosynthetic pathways and functions of ascaroside signaling molecules in the nematode Caenorhabditis elegans have been studied to better understand complex, integrative developmental decision-making. Although it is known that ascarosides play multiple roles in the development and behavior of nematode species other than C. elegans, these parallel pheromone systems have not been well-studied. Here, we show that ascarosides in the nematode Caenorhabditis briggsae are biosynthesized in the same manner as C. elegans and act to induce the alternative developmental pathway that generates the stress-resistant dauer lifestage. We show that ascr#2 is the primary component of crude dauer pheromone in C. briggsae; in contrast, C. elegans dauer pheromone relies on a combination of ascr#2, ascr#3, and several other components. We further demonstrate that Cbr-daf-22, like its C. elegans ortholog Cel-daf-22, is necessary to produce short-chain ascarosides. Moreover, Cbr-daf-22 and Cel-daf-22 mutants produce an ascaroside-independent metabolite that acts antagonistically to crude dauer pheromone and inhibits dauer formation.
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Affiliation(s)
- Sarah M Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Chester J J Wrobel
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Sharan J Prakash
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Xie K, Liu Y, Li X, Zhang H, Zhang S, Mak HY, Liu P. Dietary S. maltophilia induces supersized lipid droplets by enhancing lipogenesis and ER-LD contacts in C. elegans. Gut Microbes 2022; 14:2013762. [PMID: 35112996 PMCID: PMC8816401 DOI: 10.1080/19490976.2021.2013762] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Dietary and symbiotic bacteria can exert powerful influence on metazoan lipid metabolism. Recent studies have emerged that microbiota have a role in animal obesity and related health disorders, but the mechanisms by which bacteria influence lipid storage in their host are unknown. To reduce the complexity of the relationship between gut microbiota and the host, Caenorhabditis elegans (C. elegans) has been chosen as a model organism to study interspecies interaction. Here, we demonstrate that feeding C. elegans with an opportunistic pathogenic bacterium Stenotrophomonas maltophilia (S. maltophilia) retards growth and promotes excessive neutral lipid storage. Gene expression analysis reveals that dietary S. maltophilia induces a lipogenic transcriptional response that includes the SREBP ortholog SBP-1, and fatty acid desaturases FAT-6 and FAT-7. Live imaging and ultrastructural analysis suggest that excess neutral lipid is stored in greatly expanded lipid droplets (LDs), as a result of enhanced endoplasmic reticulum (ER)-LD interaction. We also report that loss of function mutations in dpy-9 in C. elegans confers resistance to S. maltophilia. Dietary S. maltophilia induces supersized LDs by enhancing lipogenesis and ER-LD contacts in C. elegans. This work delineates a new model for understanding microbial regulation of metazoan physiology.
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Affiliation(s)
- Kang Xie
- National Laboratory of Biomacromolecules, Cas Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences, Beijing, China
| | - Yangli Liu
- National Laboratory of Biomacromolecules, Cas Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences, Beijing, China
| | - Xixia Li
- National Laboratory of Biomacromolecules, Cas Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, Cas Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences, Beijing, China
| | - Shuyan Zhang
- National Laboratory of Biomacromolecules, Cas Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ho Yi Mak
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Pingsheng Liu
- National Laboratory of Biomacromolecules, Cas Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences, Beijing, China,CONTACT Pingsheng Liu National Laboratory of Biomacromolecules, Cas Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
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Crombie TA, Battlay P, Tanny RE, Evans KS, Buchanan CM, Cook DE, Dilks CM, Stinson LA, Zdraljevic S, Zhang G, Roberto NM, Lee D, Ailion M, Hodgins KA, Andersen EC. Local adaptation and spatiotemporal patterns of genetic diversity revealed by repeated sampling of Caenorhabditis elegans across the Hawaiian Islands. Mol Ecol 2022; 31:2327-2347. [PMID: 35167162 PMCID: PMC9306471 DOI: 10.1111/mec.16400] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/23/2022] [Accepted: 02/03/2022] [Indexed: 11/28/2022]
Abstract
The nematode Caenorhabditis elegans is among the most widely studied organisms, but relatively little is known about its natural ecology. Genetic diversity is low across much of the globe but high in the Hawaiian Islands and across the Pacific Rim. To characterize the niche and genetic diversity of C. elegans on the Hawaiian Islands and to explore how genetic diversity might be influenced by local adaptation, we repeatedly sampled nematodes over a three‐year period, measured various environmental parameters at each sampling site, and whole‐genome sequenced the C. elegans isolates that we identified. We found that the typical Hawaiian C. elegans niche comprises moderately moist native forests at high elevations (500–1,500 m) where ambient air temperatures are cool (15–20°C). Compared to other Caenorhabditis species found on the Hawaiian Islands (e.g., Caenorhabditis briggsae and Caenorhabditis tropicalis), we found that C. elegans were enriched in native habitats. We measured levels of genetic diversity and differentiation among Hawaiian C. elegans and found evidence of seven genetically distinct groups distributed across the islands. Then, we scanned these genomes for signatures of local adaptation and identified 18 distinct regions that overlap with hyper‐divergent regions, which may be maintained by balancing selection and are enriched for genes related to environmental sensing, xenobiotic detoxification, and pathogen resistance. These results provide strong evidence of local adaptation among Hawaiian C. elegans and contribute to our understanding of the forces that shape genetic diversity on the most remote volcanic archipelago in the world.
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Affiliation(s)
- Timothy A Crombie
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Paul Battlay
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Robyn E Tanny
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Kathryn S Evans
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Claire M Buchanan
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Daniel E Cook
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Clayton M Dilks
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Loraina A Stinson
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Stefan Zdraljevic
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Gaotian Zhang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Nicole M Roberto
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Daehan Lee
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Michael Ailion
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
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46
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Scharf A, Mitteldorf J, Armstead B, Schneider D, Jin H, Kocsisova Z, Tan CH, Sanchez F, Brady B, Ram N, DiAntonio GB, Wilson AM, Kornfeld K. A laboratory and simulation platform to integrate individual life history traits and population dynamics. NATURE COMPUTATIONAL SCIENCE 2022; 2:90-101. [PMID: 37981946 PMCID: PMC10655596 DOI: 10.1038/s43588-022-00190-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 01/06/2022] [Indexed: 11/21/2023]
Abstract
Understanding populations is important because they are a fundamental level of biological organization. Individual traits such as aging and lifespan interact in complex ways to determine birth and death and thereby influence population dynamics. However, we lack a deep understanding of the relationships between individual traits and population dynamics. To address this challenge, we established a laboratory population using the model organism C. elegans and an individual-based computational simulation informed by measurements of real worms. The simulation realistically models individual worms and the behavior of the laboratory population. To elucidate the role of aging in population dynamics, we analyzed old age as a cause of death and showed, using computer simulations, that it was influenced by maximum lifespan, rate of adult culling, and progeny number/food stability. Notably, populations displayed a tipping point for aging as the primary cause of adult death. Our work establishes a conceptual framework that could be used for better understanding why certain animals die of old age in the wild.
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Affiliation(s)
- Andrea Scharf
- Department of Developmental Biology, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110
| | - Josh Mitteldorf
- Department of Developmental Biology, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110
| | - Brinda Armstead
- Department of Developmental Biology, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110
| | - Daniel Schneider
- Department of Developmental Biology, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110
| | - He Jin
- Department of Developmental Biology, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110
| | - Zuzana Kocsisova
- Department of Developmental Biology, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110
| | - Chieh-Hsiang Tan
- Department of Developmental Biology, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110
- Current address: Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA 91125, USA
| | - Francesca Sanchez
- Department of Developmental Biology, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110
| | - Brian Brady
- Department of Developmental Biology, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110
| | - Natasha Ram
- Department of Developmental Biology, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110
| | - Gabriel B. DiAntonio
- Department of Developmental Biology, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110
| | - Andrea M. Wilson
- Center for the Study of Collaboration, 9378 Olive Blvd., Ste 122, Saint Louis, MO 63132
| | - Kerry Kornfeld
- Department of Developmental Biology, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110
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47
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Niu Q, Liu S, Yin M, Lei S, Rezzonico F, Zhang L. Phytobacter diazotrophicus from Intestine of Caenorhabditis elegans Confers Colonization-Resistance against Bacillus nematocida Using Flagellin (FliC) as an Inhibition Factor. Pathogens 2022; 11:pathogens11010082. [PMID: 35056030 PMCID: PMC8778419 DOI: 10.3390/pathogens11010082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 12/04/2022] Open
Abstract
Symbiotic microorganisms in the intestinal tract can influence the general fitness of their hosts and contribute to protecting them against invading pathogens. In this study, we obtained isolate Phytobacter diazotrophicus SCO41 from the gut of free-living nematode Caenorhabditis elegans that displayed strong colonization-resistance against invading biocontrol bacterium Bacillus nematocida B16. The colonization-resistance phenotype was found to be mediated by a 37-kDa extracellular protein that was identified as flagellin (FliC). With the help of genome information, the fliC gene was cloned and heterologously expressed in E. coli. It could be shown that the B. nematocida B16 grows in chains rather than in planktonic form in the presence of FliC. Scanning Electronic Microscopy results showed that protein FliC-treated B16 bacterial cells are thinner and longer than normal cells. Localization experiments confirmed that the protein FliC is localized in both the cytoplasm and the cell membrane of B16 strain, in the latter especially at the position of cell division. ZDOCK analysis showed that FliC could bind with serine/threonine protein kinase, membrane protein insertase YidC and redox membrane protein CydB. It was inferred that FliC interferes with cell division of B. nematocidal B16, therefore inhibiting its colonization of C. elegans intestines in vivo. The isolation of P. diazotrophicus as part of the gut microbiome of C. elegans not only provides interesting insights about the lifestyle of this nitrogen-fixing bacterium, but also reveals how the composition of the natural gut microbiota of nematodes can affect biological control efforts by protecting the host from its natural enemies.
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Affiliation(s)
- Qiuhong Niu
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China
| | - Suyao Liu
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China
| | - Mingshen Yin
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China
| | - Shengwei Lei
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland
| | - Lin Zhang
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China
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48
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Ma X, Hou M, Liu C, Li J, Ba Q, Wang H. Cadmium accelerates bacterial oleic acid production to promote fat accumulation in Caenorhabditis elegans. JOURNAL OF HAZARDOUS MATERIALS 2022; 421:126723. [PMID: 34325294 DOI: 10.1016/j.jhazmat.2021.126723] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/30/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Environmental cadmium, with a high dietary intake and long biological half-life, is a severe health risk by harming physiological function directly or through gut microbiota. However, the toxicity mechanisms of environmental cadmium on microbes and host systems remain unclear. Herein, we established three C. elegans and E. coli cultivated systems to investigate the vital role of microorganisms in cadmium-induced lipid toxicity and depict the interaction between environmental cadmium, bacteria, and the host. We found that only nematodes in the system with live bacteria, rather than UV-killed bacteria or no bacteria, could be induced to fat accumulation by cadmium exposure, suggesting that bacteria mediated the effect of environmental cadmium on body fat. Cadmium caused perturbation of metabolite in bacteria, most notably oleic acid, elevated the synthesis genes expression, and enhanced the bacterial oleic acid production, which further promoted the expression of lipid metabolism-related genes and fat deposition in C. elegans regardless of the cultivated system. Finally, we showed the potential protective effect of Vitamin D3 which prevented cadmium- or oleic acid-induced fat storage significantly. In conclusion, this study illustrates the mechanism underlying cadmium-induced lipid accumulation in body through bacterial metabolites and reveals the interplay between environmental cadmium, microorganisms, and the host.
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Affiliation(s)
- Xueqi Ma
- CAS Key Laboratory of Nutrition, Metabolism and Food safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200025, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 200025, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Hou
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chaobao Liu
- CAS Key Laboratory of Nutrition, Metabolism and Food safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200025, China
| | - Jingquan Li
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Qian Ba
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Hui Wang
- CAS Key Laboratory of Nutrition, Metabolism and Food safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200025, China; State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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49
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Abstract
Wild populations of the model organism C. elegans represent a valuable resource, allowing for genetic characterization underlying natural phenotypic variation. Here we provide a simple protocol on how to sample and rapidly identify C. elegans wild isolates. We outline how to find suitable habitats and organic substrates, followed by describing isolation and identification of C. elegans live cultures based on easily recognizable morphological characteristics, molecular barcodes, and mating tests. This protocol uses standard laboratory equipment and requires little prior knowledge of C. elegans biology.
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Affiliation(s)
| | - Nausicaa Poullet
- Université Côte d'Azur, CNRS, Inserm, IBV, Nice, France
- URZ, INRAE, Petit-Bourg (Guadeloupe), France
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50
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Schiffer JA, Stumbur SV, Seyedolmohadesin M, Xu Y, Serkin WT, McGowan NG, Banjo O, Torkashvand M, Lin A, Hosea CN, Assié A, Samuel BS, O’Donnell MP, Venkatachalam V, Apfeld J. Modulation of sensory perception by hydrogen peroxide enables Caenorhabditis elegans to find a niche that provides both food and protection from hydrogen peroxide. PLoS Pathog 2021; 17:e1010112. [PMID: 34941962 PMCID: PMC8699984 DOI: 10.1371/journal.ppat.1010112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/14/2021] [Indexed: 02/07/2023] Open
Abstract
Hydrogen peroxide (H2O2) is the most common chemical threat that organisms face. Here, we show that H2O2 alters the bacterial food preference of Caenorhabditis elegans, enabling the nematodes to find a safe environment with food. H2O2 induces the nematodes to leave food patches of laboratory and microbiome bacteria when those bacterial communities have insufficient H2O2-degrading capacity. The nematode's behavior is directed by H2O2-sensing neurons that promote escape from H2O2 and by bacteria-sensing neurons that promote attraction to bacteria. However, the input for H2O2-sensing neurons is removed by bacterial H2O2-degrading enzymes and the bacteria-sensing neurons' perception of bacteria is prevented by H2O2. The resulting cross-attenuation provides a general mechanism that ensures the nematode's behavior is faithful to the lethal threat of hydrogen peroxide, increasing the nematode's chances of finding a niche that provides both food and protection from hydrogen peroxide.
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Affiliation(s)
- Jodie A. Schiffer
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Stephanie V. Stumbur
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Maedeh Seyedolmohadesin
- Physics Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Yuyan Xu
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
| | - William T. Serkin
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Natalie G. McGowan
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Oluwatosin Banjo
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Mahdi Torkashvand
- Physics Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Albert Lin
- Department of Physics, Center for Brain Science, Harvard University, Cambridge, Massachusetts, United States of America
| | - Ciara N. Hosea
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Adrien Assié
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Buck S. Samuel
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Michael P. O’Donnell
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Vivek Venkatachalam
- Physics Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Javier Apfeld
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
- Bioengineering Department, Northeastern University, Boston, Massachusetts, United States of America
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